After the Arab Uprisings of 2011, the position of the Muslim Brotherhood in the Middle East changed dramatically, especially in the Persian Gulf subregion. For decades, the Muslim Brotherhood was a close ally of the Gulf monarch families because it provided a common narrative against Naser’s Pan-Arabism. The Muslim Brotherhood was also legitimising the monarch families’ right to rule. In the post-Arab Uprisings era the organisation is seen as a rival of those families and a challenge for their legitimacy to rule as it calls for political changes. The only exception was Qatar, which supported the Muslim Brotherhood financially, militarily and politically in Egypt and elsewhere. Because of that Qatar found itself at odds with the other Gulf Cooperation Council members, most notably Saudi Arabia, the UAE and Bahrain. Furthermore, the Qatar-based Al-Jazeera network spread the Brotherhood’s agenda, which was based on the call for changes due to the fact that the three abovementioned states deemed the Muslim Brotherhood a terrorist organisation. All these incidents led Saudi Arabia, the UAE and Bahrain to recall their ambassadors from Doha. Not only the Muslim Brotherhood was under pressure. It became clear that other Islamist organisations in the region had suffered from some setbacks that had affected their overall stance and performance throughout the Middle East (i.e. Hizb an-Nahda in Tunisia, Hamas in the Palestine Autonomy, the Muslim Brotherhood in Egypt). What is emphasised by analysts is that this conflict between Qatar and Saudi Arabia was a battle for regional leadership, not the first one and surely not the last (the war in Syria, the Islamic State, etc.). The aim of the paper is to present the history of the mutual relations between the Muslim Brotherhood and the Arab Gulf states, describe causes which led to the conflict, the divisions created by the conflict and the consequences of the crisis for the organisation.